2P3Z

Crystal structure of L-Rhamnonate dehydratase from Salmonella typhimurium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729560% v/v tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 272.248α = 90
b = 272.248β = 90
c = 272.248γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSGX-CAT2006-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97900APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.775099.90.0868.321.183847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.831000.67816.38274

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GSH1.819.657413938730.203510.200970.25235RANDOM26.298
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg18.084
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg6.551
r_scangle_it4.468
r_scbond_it2.935
r_angle_refined_deg1.788
r_mcangle_it1.736
r_mcbond_it1.078
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg18.084
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg6.551
r_scangle_it4.468
r_scbond_it2.935
r_angle_refined_deg1.788
r_mcangle_it1.736
r_mcbond_it1.078
r_nbtor_refined0.312
r_symmetry_vdw_refined0.229
r_nbd_refined0.22
r_xyhbond_nbd_refined0.198
r_metal_ion_refined0.181
r_symmetry_hbond_refined0.173
r_chiral_restr0.13
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6273
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
SHELXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing